Related papers: Statistical Mechanics of DNA Mutation using SUSY Q…
We introduce a model for simulating mutation of prokaryote DNA sequences. Using that model we can then evaluated traditional techniques like parsimony and maximum likelihood methods for computing phylogenetic relationships. We also use the…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…
We study the effect of the composition of the genetic sequence on the melting temperature of double stranded DNA, using some simple analytically solvable models proposed in the framework of the wetting problem. We review previous work on…
The N=2 supersymmetry in quantum mechanics involving two-component eigenfunction is investigated.
We generalize the Poland-Scheraga (PS) model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional…
We study a bijective map from integer partitions to the prime factorizations of integers that we call the "supernorm" of a partition, in which the multiplicities of the parts of partitions are mapped to the multiplicities of prime factors…
We study the internal resonance, energy transfer, activation mechanism, and control of a model of DNA division via parametric resonance. While the system is robust to noise, this study shows that it is sensitive to specific fine scale modes…
We study possible factorizations of supersymmetric (SUSY) transformations in the one-dimensional quantum mechanics into chains of elementary Darboux transformations with nonsingular coefficients. A classification of irreducible (almost)…
In a multicellular organism different cell types express a gene in different amounts. Samples from which gene expression levels can be measured typically contain a mixture of different cell types, the resulting measurements thus give only…
We used the Transfer-Integral method to compute, with an uncertainty smaller than 5%, the six fundamental characteristic exponents of two dynamical models for DNA thermal denaturation and investigate the validity of the scaling laws. Doubts…
Two different approaches are formulated to analyze two-dimensional quantum models which are not amenable to standard separation of variables. Both methods are essentially based on supersymmetrical second order intertwining relations and…
The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated…
The interaction between proteins and nucleic acids is crucial for processes that sustain cellular function, including DNA maintenance and the regulation of gene expression and translation. Amino acid mutations in protein-nucleic acid…
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively…
Two known 2-dim SUSY quantum mechanical constructions - the direct generalization of SUSY with first-order supercharges and Higher order SUSY with second order supercharges - are combined for a class of 2-dim quantum models, which {\it are…
The Poland-Scheraga model for DNA denaturation, besides playing a central role in applications, has been widely studied in the physical and mathematical literature over the past decades. More recently a natural generalization has been…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
Nonlinear molecular excitations in DNA have traditionally been modelled using the nonlinear Schr\"odinger equation (NLSE). An alternative approach is based on the plane-base rotator model and the SU(2)/U(1) generalized spin coherent states,…